Group of subjects: basic / professional

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1 Academic Year: 2012/2013 Group of subjects: basic / professional Catalogue number: Module title 1) : Polish Translation 3) : Veterinary microbiology Mikrobiologia weterynaryjna ECTS 2) 10 Faculty 4) : Faculty of Veterinary Medicine Person in charge of the module 5) : Prof. dr hab. Marian Binek Dr hab. Marcin Bańbura prof. nadzw., dr hab. Bożena Dworecka Kaszak Teachers responsible for laboratory classes, workshops and seminars 6) : prof.nadzw., dr hab. Felix Toka, dr wet. Magdalena Kizerwetter-Świda, dr wet. Małgorzata Gieryńska, dr wet. Agnieszka Sałamaszyńska-Guz, dr wet. Małgorzata Biegańska, mgr Dorota Chrobak, Unit responsible for the module 7) : Department of Preclinical Science, Faculty of Veterinary Medicine Faculty in charge 8) : Faculty of Veterinary Medicine Module status 9) : a) mandatory b) stage 1 Year: second Teaching cycle 10) Semester: winter / Module language 11) : : summer English The purpose of the veterinary microbiology module is to give the prospective veterinary surgeon adequate knowledge and skills that are applicable to veterinary medicine. Emphasis is placed on understanding the nature of infectious organisms, mechanisms by which they cause disease and how the host responds to infection. Veterinary medicine students are expected to learn the role of microbiota in health and disease, recognize the importance Objectives of the module 12) : of biosecurity, public health threat posed by zoonotic diseases, and microbial contamination of food of animal origin. The program is designed to integrate bacteriology, mycology and virology. Also an opportunity is provided for student to practice basic laboratory techniques and procedures used in diagnostics of microbial disease. The course is designed to enable the student fulfil the national and EU educational requirements and achieve competence in veterinary microbiology. a) Lectures 60 hours Teaching forms and number of hours 13) : b) Laboratory exercises 90 hours Teaching methods 14) : Detailed module description15): Lectures: the lectures emphasize selected aspects in basic and pathogenic bacteriology, mycology and virology presented in Power Point format, deal with the basic characteristics of animal pathogens, mechanisms of pathogenesis and how these relate to symptoms and laboratory diagnosis. Lectures are intended to provide illustration, clarification and update information that is further reinforcement with laboratory exercises. Laboratory exercises: individual students carry out scheduled tasks under instruction and supervision of qualified teaching staff. Exercises are performed in adequately equipped laboratories to ensure full training in all areas of veterinary microbiology. Lectures: Introduction to microbiology. An overview of microbial life. Microbial diversity, natural environments. Cell structure and evolutionary history. Bacterial cell structural organization and function. Microbial physiology: Bacterial sources of energy. Major catabolic pathways, aerobic respiration, anaerobic energy transformation (anaerobic respiration, fermentation), biosynthesis. Control of microorganisms: Physical methods of controlling microorganisms. Use of chemicals in antisepsis, disinfection and sterilization. Characteristics, modes of action and selection of chemical disinfectants. Microbial genetics selected aspects. Microbial DNA and RNA as material for in vitro manipulation. Vectors used in molecular cloning, gene bank construction. Molecular biology methods for

2 laboratory diagnostics and prophylaxis in bacterial diseases. Microorganisms and infectious diseases: pathogenesis of bacterial infections. Antimicrobial agents and chemotherapy. Antimicrobial drug resistance. Microbial systematics, nomenclature and Bergey s Manual. Bacteria of veterinary importance. Rickettsiales, Chlamydia and Chlamydophila, Spirochaetes. Genera: Treponema, Serpulina, Leptospira and Borrelia. Microaerophilic, motile helical/vibrioid Gram-negative rods. Genera: Campylobacter and Helicobacter. Gram-negative, aerobic/microaerophilic rods and cocci. Genera: Bartonella, Bordetella, Brucella, Burkholderia, Coxiella, Francisella, Moraxella, Pseudomonas, Taylorella. Facultatively anaerobic Gram-negative rods. Family: Enterobacteriaceae, Genera: Salmonella, Shigella, Yersinia, Escherichia, Klebsiella, Proteus, Enterobacter, Family: Vibrionaceae, Genera: Aeromonas, Plesiomonas, Vibrio. Family: Pasteurellaceae. Genera: Pasteurella, Mannheimia, Actinobacillus, Haemophilus and Histophilus. Obligatory anaerobic Gram-negative rods. Genera: Dichelobacter, Bacteroides, Porphyromonas, Prevotella, Fusobacterium and Streptobacillus. Infrequently encountered Gram-negative rods. Genera: Gallibacterium, Ornithobacterium, Riemerella and Lawsonia. Synergic interaction. Taxonomy; General characteristics, habitat and epidemiology, pathogenicity and pathogenesis, clinical infections, diagnostic procedures. Gram-positive cocci. Genera: Staphylococcus, Streptococcus, Enterococcus and Peptostreptococcus. Bovine mastitis caused by bacteria. Mammary gland defense mechanisms natural barriers, soluble non specific antibacterial factors. Somatic cell counts. Mastitis designation (contagious, environmental, summer mastitis). Laboratory diagnosis, treatment of mastitis, prevention and control. Non-spore-forming, regular, and irregular, facultatively anaerobic Grampositive rods. Genera: Listeria, Erysipelotrix, Actinomyces, Arcanobacterium and Trueperella. Taxonomy, general characteristics, habitat and epidemiology, pathogenicity and pathogenesis, clinical infections, diagnostic procedures. Anaerobic Gram-positive rods and cocci. Genus Clostridium (neurotoxic, histotoxic, enteric and enterotoxemic clostridia). Aerobic and facultatively anaerobic, Gram-positive spore-forming rods. Genera: Bacillus and Paenibacillus. Taxonomy, general characteristics, habitat and epidemiology, pathogenicity and pathogenesis, clinical infections, diagnostic procedures. Diptheroidal and acid fast Gram-positive rods. Genera: Corynebacterium and Mycobacterium. Taxonomy, general characteristics, habitat and epidemiology, pathogenicity and pathogenesis, clinical infections, diagnostic procedures. Gram-positive, branching, filamentous rods. Actinomycete group. Genera: Nocardia, Rhodococcus, Dermatophilus, Streptomyces. Bacteria without a cell wall. Genera: Mycoplasma and Ureaplasma. Taxonomy, general characteristics, habitat and epidemiology, pathogenicity and pathogenesis, clinical infections, diagnostic procedures Ruminants and swine intestinal tract autochthonic microflora. Rumen bacteria, and their function. Introduction to mycology; general fungal biology, ecology and morphology. Fungal spreading and sexual or asexual reproduction. Taxonomy and classification of fungi. Pathogenesis of fungal diseases. Dermatomycoses. Pathological

3 mechanisms of fungal systemic mycoses. Further cases of opportunistic mycoses - exotic and rare mycoses. Mycotoxins and mycotoxicoses. Sick building syndrome and fungal Volatile Organic Compounds Introduction to virology virus as a subcellular, infectious biological microstructure. Basic definitions. Viruses vs microorganisms. Virion morphology. Virus replication types of infection and their consequences on cells. Productive and non-productive infection. Latency. Viral oncogenesis. Characteristics of viral transformatiom of the cell. Properties of transformed cells. Reverse transcribing viruses retro- and hepadna replication and transforming potential. Subviral infectious agents basic biological properties. Prions basic properties and replication. Basic properties of selected important viruses infecting animals. Laboratory Exercises: Course organization. Safety in the Laboratory: laboratory design and safety procedures. Techniques used in bacteriological examination. Microscopes and microscopy. Application of the light microscope. Observing bacteria with the light microscope. Staining: simple stains and differential stains. Gram stain, acid-fast stain procedure, spore stain, dark field microscopy, phase-contrast microscopy. Microbial growth and cultivation techniques: chemical and physical factors affecting growth, inoculation and transfer techniques, isolation of pure bacterial cultures. Primary identification of bacteria. Measuring microbial growth. Direct measurements of microbial growth: total and viable counts. Indirect measurements of microbial growth: turbidity. Biochemical tests for the identification of bacteria. Conventional and miniaturized methods for the identification of bacteria Physical and chemical methods of controlling microorganisms: sterilization, disinfection and antisepsis Laboratory animal bioassays. Dosis minima letalis (minimum lethal dose; MLD, LD100, median lethal dose LD50), Dosis minima infectiosa (DMI, ID100,ID50) Modern methods in laboratory diagnostics of bacterial infections based on the nucleic acid analysis, plasmid DNA isolation, gel electrophoresis, PCR method, Hybridization (molecular probes). DNA sequencing. Recognition and differentiation of members of the Rickettsiales and Chlamydiales Spirochaetes: Diagnostic procedures for leptospirosis, boreliosis and swine dysentery. Differentiation of campylobacter species, diagnosis of intestinal campylobacteriosis Laboratory diagnosis of disease caused by Brucella serological tests. Laboratory identification of nonfermentative Gram-negative rods. Pseudomonas and other Pseudomonas species. Laboratory identification of Enterobacteriaceae. Isolation of Enterobacteriaceae from clinical material. General phenotypic features shared by Enterobacteriaceae. Differentiation of Enterobacteriaceae, tests on conventional media and API 20E strip. General antigenic features of Enterobacteriaceae, serological characterization of Salmonella species. Indicators of fecal pollution of water. Contamination detection. Diagnostic procedures for pasteurellosis, actinomycosis and diseases caused by Haemophilus species. Specimen collection, direct microscopy, isolation, identification, biochemical profiles. Gram-negative anaerobic bacteria of veterinary importance. Growth requirement, choice of specimens, collection and transport, methods for anaerobic culture, identification. Differentiation of staphylococci and streptococci. Conventional tests (growth

4 Formal prerequisites 16) : Initial requirements 17) : Learning outcomes18): characteristics, colony morphology, pattern of haemolysis, catalase, OFtest, coagulase, Lancefield grouping and others) and miniaturized biochemical system (API). Diagnostic procedures for pyoderma and mastitis. Morphology and growth characteristics of Listera species, Erysipelothrix rhusiopatiae, Actinomyces viscosus and Arcanobacterium pyogenes. Microscopic appearance, biochemical and other tests. Collection and transportation of specimens. Diagnostic procedures for listeriosis, erysipelas, actinomycosis and diseases caused by Trueperella pyogenes. Morphology of Clostridium species. Microscopic appearance, biochemical and other tests. Collection and transportation of specimens. Methods and techniques for laboratory diagnosis of clostridial neurointoxications, histotoxic and gastrointestinal infections. Morphology and growth characteristics of Bacillus. Diagnosis of anthrax. Morphology and growth characteristics of Mycobacterium and Corynebacterium species. Microscopic appearance, biochemical and other tests. Collection and transportation of specimens. Diagnostic procedures for caseous lymphadenitis and tuberculosis. Morphology and growth characteristics of Rhodococcus equi and Mycoplasma spp. Microscopic appearance, biochemical and other tests. Collection and transportation of specimens. Diagnostic procedures for rhodococcosis and mycoplasmosis. Morphology and growth characteristics of rumen and intestinal tract bacteria. Basic techniques employed in mycology routine diagnostics: specimen collection. Diagnosis of dermatophytoses; direct slides in investigation of skin scraping (alkaline KOH method). Co-cultivating and Micro-cultures of hyphae producing fungi. Hair perforation test, Hair coat testing under Wood s UV lamp. Slides from dermatophyte colonies. Differentiation of hyphae and spore morphology type (micro- and macroconidia, artrospores). Molds and mycotoxins. Investigation of environmental or food samples for molds, qualitative and quantitative methods. Review of techniques useful for mycotoxin detection and identification, example of biological testing for mycotoxin toxicity. Morphology of molds. Genetic and serological methods for identification and differentiation of fungi and fungal infections (review). Yeast, yeast-like and dimorphic fungi. Techniques used in cultivation and biochemical differentiation: Germ tube test, chlamydospore formation, ascus formation, utilization of sugars and chromogenic substrates, latex serology test, rapid tests from API family, drug sensitivity tests including e-tests. Investigation of smears from otitis externa cases ear canal (dogs or cats) Direct slide and cultivation, investigation of milk samples from mastitis cases. Bacterial viruses, phage-typing. Basic virological techniques virus propagation in cell culture; cell culture preparation and infection; outcome of infection cytopathic effect Basic virological techniques virus propagation in the embryonated egg; embryo infection and outcome; viral hemagglutination; inclusion bodies. Laboratory practical examination Completed and passed exams from chemistry, biophysics, histology, cell biology and genetics. Basic knowledge and skills from chemistry, biophysics, histology, cell biology Conceptual objectives: 01 - Knowledge of the structure of bacterial and fungal cells, virus particles as well as how the genetic Laboratory skills: 06 Able to follow safety rules for handling clinical or laboratory specimens contain pathogens.

5 Assessment methods 19) : Formal documentation of the learning outcome 20) : Elements impelling final grade 21) : material is organized, and what implications this has for virulence and chemotherapeutics resistance Understanding the physiology of microbial growth including how this is influenced by changes in the local environment Understanding the continuum from microbial colonization to infection to disease. Be familiar with microbial virulency. Understanding the role of microbes in health maintenance Knowledge of principals of antimicrobial function, understanding the specifics of antibiotic usage and how antibiotic resistance is acquired Knowledge of scientific names of the most significant disease causing agents and the associated diseases. Understanding the epidemiology of infectious diseases and the role of microbes in public health issues. 07 Acquisition of skill to aseptically and properly process clinical specimens Performs and interprets microbiology testing in the microbiology laboratory. 09 Recognition of the unique identifying characteristics of pathogens and names of the associated agent(s) Competence in detection and identification of microorganisms and determination of epidemiologic links between isolates Ability to perform and interpret an antibiotic susceptibility test Ability to interpret microbiological testing of air, water, animal environment and animal feed. Student performance will be evaluated by 3 in-class progressive assessments in each semester, laboratory practical examination in the fourth semester and a final exam (Conceptial and Laboratory skills: 01, 02, 03, 04, 05, 06, 07, 08, 09, 10, 11, 12). In-class progressive assessments: 6 questions worth 2 points each. Final exam: 3 questions worth 2 points each. The examination consists of review questions. The examination must be completed as scheduled. Re-scheduling will be allowed only in serious, unavoidable circumstances. Grades for the course will be assigned as follows: S= 58%, U = 58%, S = satisfactory, U = unsatisfactory The grades are based on the points earned. Grade Points 3,0 7,0 3,5 8,0-9,0 4,0 10,0 4,5 11,0 5,0 12,0 Signed written tests, laboratory practical examination protocol, exam protocol and exam papers signed by students To obtain a positive grade the student should fulfill the conditions listed below: % of the total number of points scored on each of the 6 inclass progressive assessments, obtain at least grade 3,0 from laboratory practical examination and % of the total number of points from the final exam. Students who did not obtain a positive grade from the verification tests and did not pass practical exam are not allowed to take the final exam Teaching base 22) Lecture hall at the Faculty of Veterinary Medicine, laboratories in the : Department of Preclinical Sciences Obligatory and supportive materials 23) : There are many reference books that may be helpful as supplemental material to lectures and laboratory exercises. A wide variety of general, allied health and health profession microbiology textbooks are available in the Faculty and University libraries. Various veterinary medical textbooks have large sections devoted to infectious diseases.

6 Within these discussions, disease, ecology, pathogenic mechanisms and other characteristics of agents are frequently reviewed. The following microbiology textbooks are suggested for further reading: 1. Quinn P.J., Carter M.E., Markey B., Carter G.R. : Clinical Veterinary Microbiology. Published in1994 by Wolf. 2. Quinn P.J., Markey B.K., Carter M.E., Donelly W.J., Leonard F.C.: Veterinary Microbiology and Microbial Disease. Blackwell Publishing, Quinn P.J., Markey B.K, Leonard F.C., Hartigan P., Fanning S., FitzPatrick E.S.: Veterinary Microbiology and Microbial Disease. Wiley-Blackwell, Songer G.J., Post K.W.: Veterinary microbiology: bacterial and fungal agents of animal disease. Elsevier, Madigan M.T., Martinko J.M.: Biology of microorganism. Pearson Prentice Hall, Salyers A.A., Whiet D.D. : Bacterial pathogenesis, a molecular approach. ASM Press, Washington, D.C Gyles C.L., Prescott J.F., Songer J.G., Thoen Ch.O.: Pathogenesis of bacterial infections in animals. Wiley-Blackwell, Giguere S., Prescott J.F., Baggot J.D., Walker R.D., Dowling.: Antimicrobial Therapy in Veterinary Medicine. Wiley-Blackwell, Annotations 24) : Quantitative summary of the module 25) : Estimated number of work hours per student (contact and self-study) essential to achieve presumed learning outcomes of the module 18) - base for quantifying ECTS 2 : Total ECTS points, accumulated by students during contact learning: Total ECTS points, accumulated by student during practical classes (laboratories, projects, seminars, etc.): 300 h 5 ECTS 5 ECTS Learning outcomes of the module relative to the learning outcomes of the subject 26) : Outcome No / symbol Learning outcomes: Knowledge of the structure of bacteria, fungus and virus particles. Organization of genetic material and its implication on virulence and chemotherapeutics resistance. Understanding the physiology of microbial growth including how this is influenced by changes in the local environment. Understanding the continuum from microbial colonization to infection to disease. Be familiar with microbial virulency. Understanding the role of microbes in health maintenance Knowledge of principals of antimicrobial function, understanding the specifics of antibiotic usage and how antibiotic resistance is acquired. Knowledge of scientific names of the most significant disease causing agents and the associated diseases. Understanding the epidemiology of infectious diseases and the role of microbes in public health issues. Relative to the learning outcomes of the subject: WW_NP8, K_KP1, WW_NP6, WW_NP7, WW_NP8 WW_NP6, WW_NP7, WW_NP8, K_KP2, K_KP6 WW_NP8, WW_NP11, K_KP2, K_KP6 WW_NP6, WW_NP7, WW_NP8, UO_Z15, K_KP2, K_KP6 06 Following safety rules for handling clinical or laboratory specimens containing pathogens. 07 Acquisition of skills to aseptically and properly process clinical specimens. 08 Performs and interprets microbiological testing in the microbiology laboratory., U_PUZ6 U_PUZ6, U_PUZ13, UO_Z15, U_PUZ6 U_PUZ7, W_NK7, 09 Recognition of unique identifying characteristics of pathogens and names associated with the

7 10 agent(s). Competence in detection and identification of microorganisms, and determination of the epidemiologic links between isolates. UO_Z15 UO_Z15, 11 Ability to perform and interpret an antibiotic susceptibility test. U_OZ1, UO_Z12 12 Ability to interpret microbiological testing of air, water, animal environment and animal feed. W_NK9, W_HŻ1, K_KP2, K_KP6